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It is another fine day in Johto. Crys walks along the seaside streets of Olivine as she listens to the afternoon news from her Pokégear radio. A report comes on to talk about sightings of three beams of light shooting out of the Burnt Tower, which are believed to be the three mythical beasts of Ecruteak who have laid dormant underground for many years. Pokémon scholars across the land are currently looking into the matter, and it has been proposed that the beasts must have awakened from their sleep for purposes which are not clear at the moment.

The news coverage ends, and Crys arrives at the contruction site of the new Olivine Battle Tower. Seeing the many Pokémon helping out in the place, Crys gets interested and walks over to a construction worker at the entrace to inquire about the status of the building. The man remarks that they plan to have the facility ready by the end of next month, and says it should attract lots of visitors to the city. Just then, a rumble is heard from inside, and another worker comes running out with an urgent look on his face. He hollers that one of their storage tanks has cracked, and tells everyone to evacuate immediately. Crude oil and liquid waste all of a sudden come gushing out of the tower entrance, and the construction worker whom Crys is talking to jumps back in shock as he is about to be hit by the flow. Fortunately, Crys lifts him and herself into the air by Naton's psychic power just in time, and lands on a safe area.

The construction workers than realize that the liquid waste has run out into the sea, and Crys sees that the water in the bay has been polluted and completely stained black. Worried about the water Pokémon inhabiting in the region, Crys thinks hard to for a solution. But then whirlpools start to appear in the sea, and a number of Qwilfishes come charging out to attack. One particular Qwilfish appears to be oversized, and Crys checks on her Pokédex to learn that the balloon Pokémon is able to increase its body volume by swallowing a large amount of water.

The giant Qwilfish fires a poison sting, and Naton quickly lifts Crys and the constuction worker away with its psychic. Crys remarks that the water Pokémon must be outraged by the pollution, and decides that the only way to pacify them at the moment is to capture them. She releases her full team, and start taking on the smaller Qwilfishes. The giant Qwilfish unleashes another poison sting, but Cubon fends them off with its thick club. Cubon then delivers a false swipe on the Qwilfish, and instantly shrinks it back to its normal size. After apologizing to the Qwilfishes for the accidental pollution, Crys throws up a handful of Pokéballs, and proceeds to kick them off, instantly capturing every single one of the wild Pokémon.

The construction worker thanks Crys, and dashes off to get help on clearing up the liquid waste they spilt. But then Crys notices that one captured Qwilfish seems unsettled in its ball, and looks over curiously at the direction it's wiggling towards. To her surprise, one baby Qwilfish is still floating weakly in the polluted sea, apparently poisoned by the liquid waste. She quickly has Naton carry it over, and decides that she has to bring it to the nearest PokémonCenter as soon as possible. Climbing onto Arcanon, Crys prepares to take off when a blue creature all of a sudden jumps in front of her to block her way.

The crystal-like Pokémon whose purple mane flows elegantly behind it slowly moves towards Crys, and without warning unleashes a blinding light that instantly brightens up the whole area. Crys watches in amusement as it turns to leave, and realizes with surprise that the baby Qwilfish she's carrying has been fully healed. The construction workers discover at the same time that the oil and waste in the sea has been completely cleared as well, and Crys knows that the creature she just encountered is no ordinary Pokémon.

Later, Crys contacts Prof. Oak via her Pokégear, and the professor remarks that he is just about to call her. Oak explains that three legendary Pokémon, namely Entei, Raikou and Suicune, have just unleashed themselves from the underground of Ecruteak's Burnt Tower, and says he hopes Crys will be able to collect data about them as well. Crys reveals that she has already encountered one of them, and starts describing the crystal-like Pokémon to the professor. Oak believes that Suicune is whom Crys has met, and Crys promises she will try her best to track it down.

With a new mission in mind, Crys climbs on Arcanon, and reaffirms her determination to fill the Pokédex with her talents and skills as a capture specialist…